Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 54 of 199
Found at i:15903738 original size:98 final size:98
Alignment explanation
Indices: 15903569--15903766 Score: 369
Period size: 98 Copynumber: 2.0 Consensus size: 98
15903559 GTACAATAAA
*
15903569 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
15903634 CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
*
15903667 ACTTTAAAAGAACATCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
*
15903732 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
15903765 AC
1 AC
15903767 GATTTTTAAA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
Found at i:15904858 original size:19 final size:19
Alignment explanation
Indices: 15904834--15904924 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
15904824 AATCATATAT
15904834 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
15904853 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
15904872 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
15904891 TCTATGATTGCATATCATA
1 TCTAAGATTGCATATCATA
15904910 TC-AAGATTGCATATC
1 TCTAAGATTGCATATC
15904925 CTCAAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
18 12 0.18
19 54 0.82
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:15904881 original size:38 final size:38
Alignment explanation
Indices: 15904811--15904924 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 38
15904801 AAATTAAATC
*
15904811 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
15904853 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
15904891 TCTATGATTGCATATCATATC-AAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
15904925 CTCAAAAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
37 13 0.19
38 37 0.55
39 3 0.04
41 4 0.06
42 10 0.15
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:15906034 original size:92 final size:90
Alignment explanation
Indices: 15905921--15906089 Score: 214
Period size: 92 Copynumber: 1.9 Consensus size: 90
15905911 TTACTGACAG
* * ** * * *
15905921 CTTTTATCTGCAAACCTGTTATGCATTTACAACCTATTGGCAGTGTATTAACCTACAAACATTGG
1 CTTTTATCTGCAAACCTGTTATGCATTCACAA-CTACTGGCAGCATATTAACATAC-AACACTAG
*
15905986 TGGTTTATCCACAACTATTATTGGCAA
64 TGGTTCATCCACAACTATTATTGGCAA
* *
15906013 CTTTTATCTGCAAATCC-GTTATGTATTCACAACTACTGGCAGCATATTAACATGCAACACTAGT
1 CTTTTATCTGCAAA-CCTGTTATGCATTCACAACTACTGGCAGCATATTAACATACAACACTAGT
15906077 GGTTCATCCACAA
65 GGTTCATCCACAA
15906090 ACTGGAGTGT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
90 19 0.29
91 18 0.27
92 27 0.41
93 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (90 bp):
CTTTTATCTGCAAACCTGTTATGCATTCACAACTACTGGCAGCATATTAACATACAACACTAGTG
GTTCATCCACAACTATTATTGGCAA
Found at i:15911972 original size:23 final size:24
Alignment explanation
Indices: 15911933--15911995 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
15911923 TTTCTAGGAA
15911933 ACCAAACAAAAACCCCTC-A-AACAAC
1 ACCAAA-AAAAA-CCCTCGAGAA-AAC
15911958 ACCAAAAAAAACCCTCGAGAAAAC
1 ACCAAAAAAAACCCTCGAGAAAAC
**
15911982 AAAAAAAAAAACCC
1 ACCAAAAAAAACCC
15911996 GAAATTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 5 0.15
24 21 0.62
25 8 0.24
ACGTcount: A:0.62, C:0.32, G:0.03, T:0.03
Consensus pattern (24 bp):
ACCAAAAAAAACCCTCGAGAAAAC
Found at i:15914047 original size:17 final size:17
Alignment explanation
Indices: 15914025--15914059 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
15914015 CTTCTGAAAA
15914025 GCTAAAAATTGCAGCTT
1 GCTAAAAATTGCAGCTT
*
15914042 GCTAAAAATTTCAGCTT
1 GCTAAAAATTGCAGCTT
15914059 G
1 G
15914060 TTCTTCACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (17 bp):
GCTAAAAATTGCAGCTT
Found at i:15920999 original size:29 final size:29
Alignment explanation
Indices: 15920956--15921064 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 29
15920946 CCTTTACTGG
* *
15920956 GATTTCCACAGAGGCCTTCCTTTGATAAA
1 GATTGCCACAAAGGCCTTCCTTTGATAAA
* *
15920985 GATTGCCACAAAGGCGTTTCC-TTG-TAGA
1 GATTGCCACAAAGGC-CTTCCTTTGATAAA
* * *
15921013 GATTTGCCACAAAGGCATT-CTTTAACAAA
1 GA-TTGCCACAAAGGCCTTCCTTTGATAAA
* *
15921042 GGTTGCCACAAAGGCCTACCTTT
1 GATTGCCACAAAGGCCTTCCTTT
15921065 CCAAAGTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.02
28 23 0.36
29 36 0.56
30 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (29 bp):
GATTGCCACAAAGGCCTTCCTTTGATAAA
Found at i:15921069 original size:28 final size:29
Alignment explanation
Indices: 15921016--15921093 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 29
15921006 TTGTAGAGAT
*
15921016 TTGCCACAAAGGCATTCTTTAACAAAG-G
1 TTGCCACAAAGGCATCCTTTAACAAAGTG
* * *
15921044 TTGCCACAAAGGCCTACCTTT-CCAAAGTT
1 TTGCCACAAAGGCAT-CCTTTAACAAAGTG
* *
15921073 TTGCCACAAAAGCATCTTTTA
1 TTGCCACAAAGGCATCCTTTA
15921094 CATTCAATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
28 23 0.57
29 17 0.43
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (29 bp):
TTGCCACAAAGGCATCCTTTAACAAAGTG
Found at i:15921335 original size:61 final size:60
Alignment explanation
Indices: 15921046--15921336 Score: 230
Period size: 61 Copynumber: 4.8 Consensus size: 60
15921036 AACAAAGGTT
* * * * * * * *
15921046 GCCACAAAGGCCTACCTTTCCAAAGTTTTGCCACAAAAG-CATCTTTTACAT-TCAATACTA
1 GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCA-AAAAGTTATCCTTTACATCT-AGTACTC
** * * * *
15921106 GCCACAAACACTTTCCTGTCCAGAGATTTACTG-C-AGAAGTTGTTCTTTACATCCAGTACTC
1 GCCACAAAGGCTTTCCTGTCCAGAG-TTT--TGCCAAAAAGTTATCCTTTACATCTAGTACTC
* * * *
15921167 ACCACAAAGGTTTTCCTATCCAGAGTTTTGCCAAAAAAGTTTTCCTTTACATCTAGTACTC
1 GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCC-AAAAAGTTATCCTTTACATCTAGTACTC
* * * * * * *
15921228 GCCACAAAGGCTTTCATGTCCAAAGTTTTACCACAAAGGTTGTCCTTTACATCTAATACTT
1 GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCA-AAAAGTTATCCTTTACATCTAGTACTC
* * *
15921289 GCCACAAAGGCTTTCCTGTCTAGAGTTTTGCCATAAAGCCTATCCTTT
1 GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCAAAAAG-TTATCCTTT
15921337 TTTGAGTGTT
Statistics
Matches: 180, Mismatches: 41, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
58 2 0.01
59 1 0.01
60 30 0.17
61 144 0.80
62 1 0.01
63 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (60 bp):
GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCAAAAAGTTATCCTTTACATCTAGTACTC
Found at i:15921335 original size:122 final size:121
Alignment explanation
Indices: 15921044--15921336 Score: 295
Period size: 122 Copynumber: 2.4 Consensus size: 121
15921034 TTAACAAAGG
* * * * *
15921044 TTGCCACAAAGGCCTACCTTTCCAAAGTTTTGCCACAAAAGC-ATCTTTTACATTCAATACTAGC
1 TTGCCACAAAGGCTTTCCTATCCAGAGTTTTGCCA-AAAAGCTATCCTTTACATTCAATACTAGC
* * ** * *
15921108 CACAAACACTTTCCTGTCCAGAGATTTACTGCAGAAGTTGTTCTTTACATCCAGTAC
65 CACAAACACTTTCATGTCCAAAGATTTACCACAGAAGTTGTCCTTTACATCCAATAC
** * * * * *
15921165 TCACCACAAAGGTTTTCCTATCCAGAGTTTTGCCAAAAAAGTTTTCCTTTACA-TCTAGTACTCG
1 TTGCCACAAAGGCTTTCCTATCCAGAGTTTTGCC-AAAAAGCTATCCTTTACATTC-AATACTAG
** * *
15921229 CCACAAAGGCTTTCATGTCCAAAGTTTTACCACA-AAGGTTGTCCTTTACATCTAATAC
64 CCACAAACACTTTCATGTCCAAAGATTTACCACAGAA-GTTGTCCTTTACATCCAATAC
* * *
15921287 TTGCCACAAAGGCTTTCCTGTCTAGAGTTTTGCCATAAAGCCTATCCTTT
1 TTGCCACAAAGGCTTTCCTATCCAGAGTTTTGCCAAAAAG-CTATCCTTT
15921337 TTTGAGTGTT
Statistics
Matches: 137, Mismatches: 30, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
121 41 0.30
122 96 0.70
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (121 bp):
TTGCCACAAAGGCTTTCCTATCCAGAGTTTTGCCAAAAAGCTATCCTTTACATTCAATACTAGCC
ACAAACACTTTCATGTCCAAAGATTTACCACAGAAGTTGTCCTTTACATCCAATAC
Found at i:15928147 original size:15 final size:15
Alignment explanation
Indices: 15928127--15928157 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15928117 TAAATATGTG
15928127 TATAATTGTGGATAC
1 TATAATTGTGGATAC
15928142 TATAATTGTGGATAC
1 TATAATTGTGGATAC
15928157 T
1 T
15928158 TTTTCCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
TATAATTGTGGATAC
Found at i:15929633 original size:24 final size:26
Alignment explanation
Indices: 15929572--15929641 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
15929562 ATATAGAGTA
* *
15929572 CGCCTCAAAGGCAATTCTTTCACAGTT
1 CGCCACAAAGGCTATTCTTTCACAG-T
*
15929599 CACCACAAAGGCTATTCTTTCA-A-T
1 CGCCACAAAGGCTATTCTTTCACAGT
*
15929623 CGCCACAAAGGCTACTCTT
1 CGCCACAAAGGCTATTCTT
15929642 AGCAGTCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
24 18 0.47
26 1 0.03
27 19 0.50
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCCACAAAGGCTATTCTTTCACAGT
Found at i:15931917 original size:27 final size:28
Alignment explanation
Indices: 15931861--15931920 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
15931851 TGCACCATTA
* *
15931861 AGGC-TTTCCTTTTATGAATTTCCATAG
1 AGGCTTTTCATTTTATGAATTGCCATAG
15931888 AGGCTTTTCATTTTA-GATATTGCCAT-G
1 AGGCTTTTCATTTTATGA-ATTGCCATAG
15931915 AGGCTT
1 AGGCTT
15931921 CCTTTATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (28 bp):
AGGCTTTTCATTTTATGAATTGCCATAG
Found at i:15931984 original size:30 final size:29
Alignment explanation
Indices: 15931950--15932067 Score: 130
Period size: 30 Copynumber: 3.9 Consensus size: 29
15931940 CAAAGGCTTT
* *
15931950 CTTTATAGAGTTTCGCCATAAACACTTTTC
1 CTTTACAGAGTTT-GCCATAAAGACTTTTC
* *
15931980 CTTTAAAGAGGTTTGCCACAAA-AGCTTTTC
1 CTTTACAGA-GTTTGCCATAAAGA-CTTTTC
* *
15932010 CTTTACAGAGTCTTGCCATAAAGGCTTTTT
1 CTTTACAGAGT-TTGCCATAAAGACTTTTC
15932040 CTTTACAGAGATTTGCCATAAAGACTTT
1 CTTTACAGAG-TTTGCCATAAAGACTTT
15932068 CATTTTCTGG
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.04
30 68 0.89
31 5 0.07
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (29 bp):
CTTTACAGAGTTTGCCATAAAGACTTTTC
Found at i:15932038 original size:60 final size:58
Alignment explanation
Indices: 15931937--15932057 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 58
15931927 TCCAAGGTCA
* * *
15931937 CCACAAAGGCTTTCTTTATAGAGTTTCGCCATAAACACTTTTCCTTTAAAGAGGTTTG
1 CCACAAAAGCTTTCTTTACAGAGTTTCGCCATAAACACTTTTCCTTTAAAGAGATTTG
** * *
15931995 CCACAAAAGCTTTTCCTTTACAGAGTCTT-GCCATAAAGGCTTTTTCTTTACAGAGATTTG
1 CCACAAAAGC-TTT-CTTTACAGAGT-TTCGCCATAAACACTTTTCCTTTAAAGAGATTTG
15932055 CCA
1 CCA
15932058 TAAAGACTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 9 0.17
59 3 0.06
60 39 0.74
61 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (58 bp):
CCACAAAAGCTTTCTTTACAGAGTTTCGCCATAAACACTTTTCCTTTAAAGAGATTTG
Found at i:15937293 original size:41 final size:41
Alignment explanation
Indices: 15937236--15937345 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
15937226 CATTGTATGT
*
15937236 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
* *
15937277 AAGGGGTTGCTAAGTGCAGATTTCCTGAATCACTAATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
* *
15937318 AAGGGGTTACTAAGTGTAGATTCCCCGA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGA
15937346 GAGGTTGCTA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
Found at i:15943507 original size:47 final size:46
Alignment explanation
Indices: 15943391--15943513 Score: 129
Period size: 47 Copynumber: 2.6 Consensus size: 46
15943381 GTATATATAA
* ** *
15943391 ATATATTTTTTATGCATGAAAATGAATTAATTTATAGCTGAATGTAT
1 ATATATTTATTATGCATG-AAATGAATTAAACTATAGCCGAATGTAT
* * * *
15943438 ATGTAATTATTATGCAGAGAAATGAATTAAACTATGGCCGAATGTAT
1 ATATATTTATTATGCA-TGAAATGAATTAAACTATAGCCGAATGTAT
* *
15943485 ATATATTTGTTATGCATTGAAATAAATTA
1 ATATATTTATTATGCA-TGAAATGAATTA
15943514 TTTGAAATTA
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
47 60 0.98
48 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (46 bp):
ATATATTTATTATGCATGAAATGAATTAAACTATAGCCGAATGTAT
Found at i:15943608 original size:157 final size:157
Alignment explanation
Indices: 15943386--15943670 Score: 464
Period size: 157 Copynumber: 1.8 Consensus size: 157
15943376 CAAATGTATA
* * * *
15943386 TATAAATATATTTTTTATGCATGAAAATGAATTAATTTATAGCTGAATGTATATGTAATTATTAT
1 TATAAATATATTTGTTATACATGAAAATGAATTAATCTATAGCTGAACGTATATGTAATTATTAT
* * *
15943451 GCAGAGAAATGAATTAAACTATGGCCGAATGTATATATATTTGTTATGCATTGAAATAAATTATT
66 GCAGAGAAATAAATTAAACTATGGCCGAATATATATATATTTGTTATACATTGAAATAAATTATT
15943516 TGAAATTACATAGGTTATGGCCGAATG
131 TGAAATTACATAGGTTATGGCCGAATG
* *
15943543 TATATATATATTTGTTATACATTG-AAATGAATTAATCTATAGCTGAACGTATATGTAATTGTTA
1 TATAAATATATTTGTTATACA-TGAAAATGAATTAATCTATAGCTGAACGTATATGTAATTATTA
*
15943607 TGCAGAGAAATAAATTAAACTATGGCCGAATATATATATATTTGTTATACATTGAAATGAATTA
65 TGCAGAGAAATAAATTAAACTATGGCCGAATATATATATATTTGTTATACATTGAAATAAATTA
15943671 ATCTATAGCT
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
157 115 0.98
158 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.39
Consensus pattern (157 bp):
TATAAATATATTTGTTATACATGAAAATGAATTAATCTATAGCTGAACGTATATGTAATTATTAT
GCAGAGAAATAAATTAAACTATGGCCGAATATATATATATTTGTTATACATTGAAATAAATTATT
TGAAATTACATAGGTTATGGCCGAATG
Found at i:15943617 original size:47 final size:47
Alignment explanation
Indices: 15943535--15943849 Score: 324
Period size: 47 Copynumber: 6.6 Consensus size: 47
15943525 ATAGGTTATG
* ** *
15943535 GCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATA
1 GCCGAATGTATATATA-A-TTGTTATGCAGAGAAATGAATTAAACTATA
* * * * *
15943584 GCTGAACGTATATGTAATTGTTATGCAGAGAAATAAATTAAACTATG
1 GCCGAATGTATATATAATTGTTATGCAGAGAAATGAATTAAACTATA
* * * ** *
15943631 GCCGAATATATATATATTTGTTATACATTGAAATGAATTAATCTATA
1 GCCGAATGTATATATAATTGTTATGCAGAGAAATGAATTAAACTATA
* * * *
15943678 GCTGAATGTATATGTAATTGTTATGCAGAGAAATAAATTAAACTATG
1 GCCGAATGTATATATAATTGTTATGCAGAGAAATGAATTAAACTATA
* ** *
15943725 GCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATA
1 GCCGAATGTATATATA-A-TTGTTATGCAGAGAAATGAATTAAACTATA
* * * * *
15943774 GCTGAATGTATATGTAATCGTTATGCAAAGAAATGAATTAAACTATG
1 GCCGAATGTATATATAATTGTTATGCAGAGAAATGAATTAAACTATA
15943821 GCCGAATGTATATATATATTTGTTATGCA
1 GCCGAATGTATATATA-A-TTGTTATGCA
15943850 TTGAAATAAA
Statistics
Matches: 213, Mismatches: 49, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
47 149 0.70
48 4 0.02
49 60 0.28
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (47 bp):
GCCGAATGTATATATAATTGTTATGCAGAGAAATGAATTAAACTATA
Found at i:15943788 original size:96 final size:96
Alignment explanation
Indices: 15943531--15943862 Score: 596
Period size: 96 Copynumber: 3.5 Consensus size: 96
15943521 TTACATAGGT
*
15943531 TATGGCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAACGTATA
1 TATGGCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATA
15943596 TGTAATTGTTATGCAGAGAAATAAATTAAAC
66 TGTAATTGTTATGCAGAGAAATAAATTAAAC
15943627 TATGGCCGAA--TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATA
1 TATGGCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATA
15943690 TGTAATTGTTATGCAGAGAAATAAATTAAAC
66 TGTAATTGTTATGCAGAGAAATAAATTAAAC
15943721 TATGGCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATA
1 TATGGCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATA
* * *
15943786 TGTAATCGTTATGCAAAGAAATGAATTAAAC
66 TGTAATTGTTATGCAGAGAAATAAATTAAAC
* *
15943817 TATGGCCGAATGTATATATATATTTGTTATGCATTGAAATAAATTA
1 TATGGCCGAATGTATATATATATTTGTTATACATTGAAATGAATTA
15943863 TTTGAAGTTA
Statistics
Matches: 228, Mismatches: 6, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
94 93 0.41
96 135 0.59
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.37
Consensus pattern (96 bp):
TATGGCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATA
TGTAATTGTTATGCAGAGAAATAAATTAAAC
Found at i:15944023 original size:41 final size:41
Alignment explanation
Indices: 15943966--15944111 Score: 213
Period size: 41 Copynumber: 3.6 Consensus size: 41
15943956 TTTTGTAAGT
*
15943966 TTGGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATGTA
1 TTGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
*
15944007 TTGGGCTTTATGCCTAGCAGGCTCTGTGCCTGTGAAATGTA
1 TTGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
** *
15944048 TCAGGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGT-
1 TTGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
* *
15944088 TTCGGGCTTTGTGTCTAGCAGGCT
1 TT-GGGCTTTATGCCTAGCAGGCT
15944112 TTATGTCGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 92 0.99
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (41 bp):
TTGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
Found at i:15944136 original size:82 final size:82
Alignment explanation
Indices: 15943969--15944141 Score: 204
Period size: 82 Copynumber: 2.1 Consensus size: 82
15943959 TGTAAGTTTG
* * *
15943969 GGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATGTATTGGGCTTTATGCCTAGCAGGCTCTGT
1 GGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGTATTGGGCTTTATGCCTAGCAGGCTCTAT
* * *
15944034 GCCTGTGAAATGTATCA
66 GCCGGTGAAATATATAA
* * *
15944051 GGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGT-TTCGGGCTTTGTGTCTAGCAGGCTTTA
1 GGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGTATT-GGGCTTTATGCCTAGCAGGCTCTA
* ***
15944115 TGTCGGTGTTTTATATAA
65 TGCCGGTGAAATATATAA
*
15944133 GGCTCTATG
1 GGCTTTATG
15944142 TTTAACAAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
81 2 0.03
82 74 0.97
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.35
Consensus pattern (82 bp):
GGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGTATTGGGCTTTATGCCTAGCAGGCTCTAT
GCCGGTGAAATATATAA
Found at i:15949260 original size:27 final size:27
Alignment explanation
Indices: 15949175--15949265 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 27
15949165 AATACACCAA
*
15949175 AAAGG-TAGTTCTTTCAGAGTTCACCAC
1 AAAGGCTA-TTCTTTCAGAGTTCGCCAC
* * * *
15949202 AAAGACTGTTCTTTTAGAGTTTGCCAC
1 AAAGGCTATTCTTTCAGAGTTCGCCAC
* * *
15949229 AAAGGTTATTCTTTCAAAGTTCGCCAT
1 AAAGGCTATTCTTTCAGAGTTCGCCAC
15949256 AAAGGCTATT
1 AAAGGCTATT
15949266 ATTAATAGTC
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (27 bp):
AAAGGCTATTCTTTCAGAGTTCGCCAC
Found at i:15950117 original size:3 final size:3
Alignment explanation
Indices: 15950109--15950145 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
15950099 ACCACTTGAG
15950109 GAA GAA GAA GAA GAA GAA GAA GAA GAA GGAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA
15950146 TCCTTTTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:15958259 original size:31 final size:31
Alignment explanation
Indices: 15958201--15958269 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
15958191 TATGTTAAAT
*
15958201 AATTATTAAATTATTTAAAAAAATTTATTCA
1 AATTATTAAATTATTCAAAAAAATTTATTCA
* * ** *
15958232 AGTTATTAAATTATTCGAAAATTTTTATTTA
1 AATTATTAAATTATTCAAAAAAATTTATTCA
15958263 AATTATT
1 AATTATT
15958270 GATTTATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
AATTATTAAATTATTCAAAAAAATTTATTCA
Found at i:15958946 original size:27 final size:27
Alignment explanation
Indices: 15958916--15958977 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
15958906 GCCACTGATA
15958916 GGCGGCACCAAAGGTGCCATTCCCATG
1 GGCGGCACCAAAGGTGCCATTCCCATG
***
15958943 GGCGGCACCGGTGGTGCCATTCCCATG
1 GGCGGCACCAAAGGTGCCATTCCCATG
15958970 GGCGGCAC
1 GGCGGCAC
15958978 TGCTCTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.34, G:0.35, T:0.15
Consensus pattern (27 bp):
GGCGGCACCAAAGGTGCCATTCCCATG
Found at i:15959056 original size:18 final size:18
Alignment explanation
Indices: 15959033--15959067 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15959023 AAGGAGAGGG
*
15959033 AAAGAAGAAGAAAGAAAT
1 AAAGAAAAAGAAAGAAAT
*
15959051 AAAGAAAAAGAAGGAAA
1 AAAGAAAAAGAAAGAAA
15959068 GAAAACGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AAAGAAAAAGAAAGAAAT
Found at i:15959103 original size:44 final size:44
Alignment explanation
Indices: 15959035--15959150 Score: 171
Period size: 44 Copynumber: 2.6 Consensus size: 44
15959025 GGAGAGGGAA
15959035 AGAAGAAGAAAGAAATAAAGAAAAAGAAGGAAAGAAAACGAAAGG
1 AGAAGAAGAAA-AAATAAAGAAAAAGAAGGAAAGAAAACGAAAGG
* * *
15959080 AGAAGAAGAAAAAATAATGAAAAATAAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAAAAAATAAAGAAAAAGAAGGAAAGAAAACGAAAGG
* *
15959124 AGAAG-AGAAAAAAAAAAGAAGAAGAAG
1 AGAAGAAGAAAAAATAAAGAAAAAGAAG
15959151 AGGGGAGGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
43 18 0.28
44 35 0.55
45 11 0.17
ACGTcount: A:0.70, C:0.01, G:0.26, T:0.03
Consensus pattern (44 bp):
AGAAGAAGAAAAAATAAAGAAAAAGAAGGAAAGAAAACGAAAGG
Found at i:15959122 original size:10 final size:11
Alignment explanation
Indices: 15959031--15959122 Score: 50
Period size: 10 Copynumber: 8.5 Consensus size: 11
15959021 AGAAGGAGAG
*
15959031 GGAAAGAAGAA
1 GGAAAGAATAA
15959042 -GAAAGAAATAA
1 GGAAAG-AATAA
* *
15959053 AGAAA-AAGAA
1 GGAAAGAATAA
15959063 GGAAAGAA-AA
1 GGAAAGAATAA
* * *
15959073 CGAAAGGAGAA
1 GGAAAGAATAA
*
15959084 GAAGAAAAAATAA
1 G--GAAAGAATAA
*
15959097 TGAAA-AATAA
1 GGAAAGAATAA
15959107 GGAAAGAA-AA
1 GGAAAGAATAA
15959117 GGAAAG
1 GGAAAG
15959123 GAGAAGAGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
10 38 0.60
11 14 0.22
12 4 0.06
13 7 0.11
ACGTcount: A:0.68, C:0.01, G:0.26, T:0.04
Consensus pattern (11 bp):
GGAAAGAATAA
Found at i:15962684 original size:18 final size:18
Alignment explanation
Indices: 15962661--15962705 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
15962651 ATCCCAATGA
15962661 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
15962679 TCGCCACCATCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
15962697 TCACCACCA
1 TCGCCACCA
15962706 ACCATATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.49, G:0.04, T:0.31
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:15963253 original size:22 final size:22
Alignment explanation
Indices: 15963225--15963377 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
15963215 TGTTGATAGT
*
15963225 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
15963247 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
15963269 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
15963291 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
15963313 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
15963335 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
15963357 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
15963378 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:15963818 original size:27 final size:27
Alignment explanation
Indices: 15963779--15963840 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
15963769 AACACGACTA
15963779 GTGCCGCCAATGGGAATGGCACCTTCG
1 GTGCCGCCAATGGGAATGGCACCTTCG
* *
15963806 GTGCCGCCCATGGGAATGGCACCTTTG
1 GTGCCGCCAATGGGAATGGCACCTTCG
15963833 GTGCCGCC
1 GTGCCGCC
15963841 TATCAGTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.15, C:0.32, G:0.34, T:0.19
Consensus pattern (27 bp):
GTGCCGCCAATGGGAATGGCACCTTCG
Found at i:15965737 original size:19 final size:19
Alignment explanation
Indices: 15965713--15965753 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
15965703 TTTTTTCGGG
*
15965713 TTTAGGGTTATGTTATAAA
1 TTTAGGATTATGTTATAAA
15965732 TTTAGGATTATGTTATAAA
1 TTTAGGATTATGTTATAAA
15965751 TTT
1 TTT
15965754 TTGTGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (19 bp):
TTTAGGATTATGTTATAAA
Found at i:15965955 original size:27 final size:27
Alignment explanation
Indices: 15965919--15965975 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
15965909 ATATCCCGAC
15965919 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
* *
15965946 ATTACAATATTCATATAAAATTGCAAT
1 ATTACAATATTCATACAAAATTACAAT
15965973 ATT
1 ATT
15965976 TTTTTGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:15966041 original size:22 final size:22
Alignment explanation
Indices: 15966016--15966102 Score: 120
Period size: 22 Copynumber: 3.7 Consensus size: 22
15966006 TCTATATTTA
15966016 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
15966038 GTATGAATATTGTAATATTATAATTTT
1 GTATGAATATTGT-A-ATT-T--TTTT
*
15966065 GTATGAATATTGCAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
15966087 GTATGAATATTGTAAT
1 GTATGAATATTGTAAT
15966103 GTCGGGATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
22 32 0.55
23 1 0.02
24 4 0.07
25 4 0.07
26 1 0.02
27 16 0.28
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (22 bp):
GTATGAATATTGTAATTTTTTT
Found at i:15966070 original size:49 final size:49
Alignment explanation
Indices: 15966009--15966149 Score: 175
Period size: 49 Copynumber: 2.9 Consensus size: 49
15965999 TAGATTATCT
* *
15966009 ATATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATAT-T
1 ATATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATGG
* *
15966057 ATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATGTCGGG
1 AT-ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATAT--GG
*
15966109 ATATATTG--T-AATATTGTAA-TTTTTTGTATGAATATTGTAAT
1 ATATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAAT
15966150 TATTTTATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
47 22 0.27
48 11 0.13
49 43 0.52
51 5 0.06
52 2 0.02
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (49 bp):
ATATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATGG
Found at i:15966360 original size:27 final size:27
Alignment explanation
Indices: 15966283--15966349 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
15966273 TAACATAAAT
* *
15966283 TTCATTGGAGCCTCTCTATAAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
15966310 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
15966337 TTCATTGGCGCCT
1 TTCATTGGCGCCT
15966350 ACCTGATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:15966425 original size:12 final size:12
Alignment explanation
Indices: 15966410--15966441 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15966400 CCGTATTTTT
15966410 TTAAAAAAATTA
1 TTAAAAAAATTA
15966422 TTAAAAAAA-TA
1 TTAAAAAAATTA
15966433 -TAAAAAAAT
1 TTAAAAAAAT
15966442 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 2 0.11
12 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:15970182 original size:15 final size:16
Alignment explanation
Indices: 15970158--15970187 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15970148 ATCATTTTAT
15970158 TTTTTCTTTTTAACTC
1 TTTTTCTTTTTAACTC
15970174 TTTTT-TTTTTAACT
1 TTTTTCTTTTTAACT
15970188 TTTGGAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTCTTTTTAACTC
Found at i:15972325 original size:2 final size:2
Alignment explanation
Indices: 15972318--15972374 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
15972308 TCTCTTCTTG
15972318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15972360 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
15972375 GGCTGCTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15976862 original size:43 final size:44
Alignment explanation
Indices: 15976814--15976992 Score: 258
Period size: 43 Copynumber: 4.2 Consensus size: 44
15976804 TTTTTAAAAT
* * *
15976814 AAACGCCGCTATAGATCATGATCTTTAGCGGCGCTT-TTCTCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACTCAC
15976857 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACT-AC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACTCAC
*
15976900 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTAC-CAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACTCAC
* * * *
15976943 AAACGTCGCTAAAGAACATGACCTTTAGCGACGCTTATAC-CAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACTCAC
15976986 AAACGCC
1 AAACGCC
15976993 ACTATAAAGA
Statistics
Matches: 124, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
43 121 0.98
44 3 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (44 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACTCAC
Found at i:15976920 original size:86 final size:85
Alignment explanation
Indices: 15976814--15977047 Score: 271
Period size: 86 Copynumber: 2.8 Consensus size: 85
15976804 TTTTTAAAAT
* *
15976814 AAACGCCGCTATAGATCATGATCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGATCATGAC
1 AAACGCCGCTAAAGATCATGA-CTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACATGAC
* * *
15976879 CTTTAGCGGCGCTTCTACTAC
65 CTTTAGCGACGCTTATACCAC
* * *
15976900 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTAC-CACAAACGTCGCTAAAGAACATGA
1 AAACGCCGCTAAAGATCATGA-CTTTAGCGGCGCTT-TTCTCACAAACGCCGCTAAAGAACATGA
15976964 CCTTTAGCGACGCTTATACCAC
64 CCTTTAGCGACGCTTATACCAC
* * * * *
15976986 AAACGCCACTATAA-A-GATGACTCTTAGCGGTGCTTTT-TGACAAATGCCGCTAAA-AACATGA
1 AAACGCCGCTA-AAGATCATGACT-TTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACATGA
15977047 C
64 C
15977048 TTTTTAAAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
83 8 0.06
84 16 0.13
85 14 0.11
86 85 0.67
87 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (85 bp):
AAACGCCGCTAAAGATCATGACTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACATGACC
TTTAGCGACGCTTATACCAC
Found at i:15978915 original size:150 final size:151
Alignment explanation
Indices: 15978638--15978917 Score: 553
Period size: 150 Copynumber: 1.9 Consensus size: 151
15978628 ACATGCTAAC
15978638 CTGTAGGTTTGTTCAATTGGCTTATTGGTTTCGTTATCTTTTGTATGCCGCCTATAACGTTCTGT
1 CTGTAGGTTTGTTCAATTGGCTTATTGGTTTCGTTATCTTTTGTATGCCGCCTATAACGTTCTGT
15978703 AGTTTGCTGCATGCTAAATAAATGATATATCCAAATAGCAACACAAATCAATGCATGGAAAAGCT
66 AGTTTGCTGCATGCTAAATAAATGATATATCCAAATAGCAACACAAATCAATGCATGGAAAAGCT
15978768 AAATAAATGATAAATAACGTT
131 AAATAAATGATAAATAACGTT
15978789 CTGTA-GTTTGTTCAATTGGCTTATTGGTTTCGTTATCTTTTGTATGCCGCCTATAACGTTCTGT
1 CTGTAGGTTTGTTCAATTGGCTTATTGGTTTCGTTATCTTTTGTATGCCGCCTATAACGTTCTGT
15978853 AGTTTGCTGCATGCTAAATAAATGATATATCCAAATAGCAACACAAATCAATGCATGGAAAAGCT
66 AGTTTGCTGCATGCTAAATAAATGATATATCCAAATAGCAACACAAATCAATGCATGGAAAAGCT
15978918 TGTAATTAAA
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
150 124 0.96
151 5 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (151 bp):
CTGTAGGTTTGTTCAATTGGCTTATTGGTTTCGTTATCTTTTGTATGCCGCCTATAACGTTCTGT
AGTTTGCTGCATGCTAAATAAATGATATATCCAAATAGCAACACAAATCAATGCATGGAAAAGCT
AAATAAATGATAAATAACGTT
Found at i:15980584 original size:22 final size:22
Alignment explanation
Indices: 15980528--15980593 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
15980518 GTATGTTTGT
* * *
15980528 AAAGTTGGGGGTTTCAAGGGGG
1 AAAGTTGGGGATTTTAGGGGGG
* * *
15980550 AAAATTAGAGATTTTAGGGGGG
1 AAAGTTGGGGATTTTAGGGGGG
*
15980572 AAAGTTGGGGA-TTTCGGGGGG
1 AAAGTTGGGGATTTTAGGGGGG
15980593 A
1 A
15980594 GGGATTTTAT
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 10 0.29
22 24 0.71
ACGTcount: A:0.27, C:0.03, G:0.45, T:0.24
Consensus pattern (22 bp):
AAAGTTGGGGATTTTAGGGGGG
Found at i:15981785 original size:7 final size:7
Alignment explanation
Indices: 15981773--15981798 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
15981763 ACCCCAAATT
15981773 CCTAACC
1 CCTAACC
15981780 CCTAACC
1 CCTAACC
15981787 CCTAACC
1 CCTAACC
15981794 CCTAA
1 CCTAA
15981799 ACATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAACC
Found at i:15981879 original size:96 final size:95
Alignment explanation
Indices: 15981707--15981880 Score: 262
Period size: 96 Copynumber: 1.8 Consensus size: 95
15981697 NNNNNNNNTC
*
15981707 TTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAACTCGACCCCAAAT
1 TTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAACTCGACACCAAAT
* * *
15981772 TCCTAACCCCTAACCCCTAACCCCTAAACA
66 ACATAAACCCTAACCCCTAACCCCTAAACA
*
15981802 TTATTTAATATATAAATTAAAACACACTAATTAATCTAAA-CCTTAAACCCTAAC-CTGACACTA
1 TTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAATCC-TAAACCCTAACTC-GACACCA
15981865 AATACATAAACCCTAA
63 AATACATAAACCCTAA
15981881 ATCCTTAACT
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
95 25 0.35
96 46 0.65
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (95 bp):
TTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAACTCGACACCAAAT
ACATAAACCCTAACCCCTAACCCCTAAACA
Found at i:15981924 original size:14 final size:14
Alignment explanation
Indices: 15981886--15981937 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
15981876 CCTAAATCCT
* *
15981886 TAACTCTTAACCTC
1 TAACCCTTAACCCC
15981900 TAA-CCTCTAACCCC
1 TAACCCT-TAACCCC
*
15981914 TAACCCTTAACCCA
1 TAACCCTTAACCCC
*
15981928 TAAACCTTAA
1 TAACCCTTAA
15981938 ATCACAACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 2 0.06
14 27 0.84
15 3 0.09
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (14 bp):
TAACCCTTAACCCC
Found at i:15981974 original size:14 final size:15
Alignment explanation
Indices: 15981957--15981989 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
15981947 CTTAAATCAG
15981957 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
15981971 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
15981986 AATC
1 AATC
15981990 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:15982454 original size:41 final size:41
Alignment explanation
Indices: 15982395--15982673 Score: 324
Period size: 41 Copynumber: 6.8 Consensus size: 41
15982385 AAATATTTTT
*
15982395 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* ** * *
15982436 GCGGCGCTTCTTGGAAAACGCTGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
15982477 GCGGCGCTTCTTAAAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * **
15982518 GTGGCGCTTTTCCAAAAACACCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * **
15982559 GCGGCACTTTTTCAAAAACGCCACTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * **
15982600 GCGGCGCATTTTCAAAAACACAGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
15982641 GCGACGCTTTTTTTAAAAACGCCGCTAAAGCCC
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAGCCC
15982674 CGTGGGCTTA
Statistics
Matches: 204, Mismatches: 33, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
41 185 0.91
42 19 0.09
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:15983280 original size:26 final size:29
Alignment explanation
Indices: 15983232--15983290 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
15983222 TTTAATTTTT
* *
15983232 TAAAAAAATATTTAATGATATTTTATTAAA
1 TAAAAAAATATTTAA-GATATTTCACTAAA
15983262 TAAAAAAATATTT-A-A-ATTTCACTAAA
1 TAAAAAAATATTTAAGATATTTCACTAAA
15983288 TAA
1 TAA
15983291 TTCTATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.44
27 1 0.04
29 1 0.04
30 13 0.48
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAAAAAATATTTAAGATATTTCACTAAA
Found at i:15988026 original size:22 final size:21
Alignment explanation
Indices: 15987978--15988026 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
15987968 AACTAAATCC
** *
15987978 TTTCTCTCAATTTTTCTCTAA
1 TTTCTCTCAATTCCTCTCAAA
15987999 TATTCTCTCAAATTCCTCTCAAA
1 T-TTCTCTC-AATTCCTCTCAAA
15988022 TTTCT
1 TTTCT
15988027 ATTTAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.48
23 11 0.48
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTCTCTCAATTCCTCTCAAA
Found at i:15989851 original size:18 final size:18
Alignment explanation
Indices: 15989828--15989871 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
15989818 ATGCCAGGTG
* *
15989828 TGTATCCTAGCCCTTTTA
1 TGTATCCTAACCCTTATA
15989846 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
15989864 TGTTTCCT
1 TGTATCCT
15989872 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:15990354 original size:49 final size:49
Alignment explanation
Indices: 15990292--15990510 Score: 377
Period size: 49 Copynumber: 4.5 Consensus size: 49
15990282 GTTTATATTA
15990292 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
15990341 ATGTAATCAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
15990390 ATGTAATAAAATACAAAATAGTTTATTTTGAATAGTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
15990439 ATTTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTT-G
*
15990489 -TTTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
15990511 AATATTCTTA
Statistics
Matches: 162, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
49 162 1.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:15993890 original size:125 final size:125
Alignment explanation
Indices: 15993638--15994019 Score: 595
Period size: 125 Copynumber: 3.1 Consensus size: 125
15993628 CCCAAACATG
* * * *
15993638 CTACTATAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATTCTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
15993703 TTGAAGC-ATTTTTATACTATTTGTTCAGAAACGTCAACTCGAAATTATTTTTTTAGGAC
66 TTGAAGCGATTTTTATACTATTTGCTCAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
* * * *
15993762 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCAATTTCAAAAATTCTTCTGATAAAGGATCCTGG
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
15993827 TTCAAGCGATTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCGATTTTTATACTATTTGCTCAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
* *
15993887 CTACTGTAGCAAAAAAGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCTTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
15993952 TTGAAGCGGTTTTTATACTATTTGCTCAGAAAAGTCAACTCAAAATTATTTTTTCAGAAC
66 TTGAAGCGATTTTTATACTATTTGCTCAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
15994012 CTACTGTA
1 CTACTGTA
15994020 ATAGGCCTAA
Statistics
Matches: 234, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
124 63 0.27
125 171 0.73
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (125 bp):
CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGATTTTTATACTATTTGCTCAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:15995877 original size:24 final size:24
Alignment explanation
Indices: 15995850--15995898 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
15995840 CTTACTTTTT
15995850 TTATATATTAGTATGTATGTATCATTA
1 TTAT-TATTA-TATGTAT-TATCATTA
*
15995877 TTATTTTTATATGTATTATCAT
1 TTATTATTATATGTATTATCAT
15995899 GTTTAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 7 0.33
26 4 0.19
27 4 0.19
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (24 bp):
TTATTATTATATGTATTATCATTA
Found at i:15997227 original size:9 final size:9
Alignment explanation
Indices: 15997210--15997255 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
15997200 TTTTTTCTCT
15997210 AAAACCCTA
1 AAAACCCTA
*
15997219 AAAATCCT-
1 AAAACCCTA
15997227 AAAACCCTA
1 AAAACCCTA
*
15997236 AAAATCCTA
1 AAAACCCTA
*
15997245 AAACCCCTA
1 AAAACCCTA
15997254 AA
1 AA
15997256 CCTTAAATCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAACCCTA
Found at i:15997230 original size:17 final size:17
Alignment explanation
Indices: 15997208--15997255 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
15997198 AATTTTTTCT
15997208 CTAAAACCCTAAAAATC
1 CTAAAACCCTAAAAATC
15997225 CTAAAACCCTAAAAATC
1 CTAAAACCCTAAAAATC
15997242 CTAAAACCCCTAAA
1 CTAAAA-CCCTAAA
15997256 CCTTAAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (17 bp):
CTAAAACCCTAAAAATC
Found at i:15999251 original size:2 final size:2
Alignment explanation
Indices: 15999244--15999295 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
15999234 TCCCATTGTA
15999244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15999286 AT AT AT AT AT
1 AT AT AT AT AT
15999296 GCGTGTCTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16002718 original size:3 final size:3
Alignment explanation
Indices: 16002710--16002746 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16002700 ATTTCTCAAC
16002710 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
16002747 TGAAATTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:16005693 original size:21 final size:23
Alignment explanation
Indices: 16005652--16005695 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
16005642 TTATATTAAA
*
16005652 TTATATTAAAAGATTTTTTATTT
1 TTATATTAAAAGATATTTTATTT
16005675 TTATATT-AAA-ATATTTTATTT
1 TTATATTAAAAGATATTTTATTT
16005696 ACTGCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 3 0.15
23 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATATTAAAAGATATTTTATTT
Found at i:16012315 original size:68 final size:69
Alignment explanation
Indices: 16012188--16012318 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 69
16012178 TAAACTTAAT
* * * *
16012188 CACTTTAATATTAAATTAATATAATATGTATCAAGATAAATATTAAATTAAATTTAATATTAAGA
1 CACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATACTAAATTAAATTAAATATTAAGA
16012253 TAAC
66 TAAC
* *
16012257 CACTTTAATATTAAATTAATAAAATA-CTATTAAGATAAGTACTAAATTAAATTAAATATTAA
1 CACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATACTAAATTAAATTAAATATTAA
16012319 ACTATTAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
68 31 0.55
69 25 0.45
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (69 bp):
CACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATACTAAATTAAATTAAATATTAAGA
TAAC
Found at i:16021309 original size:27 final size:28
Alignment explanation
Indices: 16021277--16021339 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
16021267 ATTTGATATA
*
16021277 AATATAAAT-TATATAATTATTATTTA-
1 AATATAAATAAATATAATTATTATTTAT
*
16021303 ACATATATAATAAATATAATTATTTTTTAT
1 A-ATATA-AATAAATATAATTATTATTTAT
16021333 AATATAA
1 AATATAA
16021340 TATATTTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 5 0.16
28 4 0.13
29 20 0.65
30 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
AATATAAATAAATATAATTATTATTTAT
Found at i:16023324 original size:31 final size:30
Alignment explanation
Indices: 16023267--16023334 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
16023257 GATGTAGCAC
*
16023267 CTGTA-TTTTAAATTGATTAATATTAGTCA
1 CTGTACTTTTAAATTGATCAATATTAGTCA
* * * *
16023296 TTGTACTTTTCAAATTGGTCAATTTTAGTCC
1 CTGTACTTTT-AAATTGATCAATATTAGTCA
16023327 CTGTACTT
1 CTGTACTT
16023335 CTTGAATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 4 0.13
30 4 0.13
31 23 0.74
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.49
Consensus pattern (30 bp):
CTGTACTTTTAAATTGATCAATATTAGTCA
Found at i:16035672 original size:15 final size:15
Alignment explanation
Indices: 16035652--16035685 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
16035642 TGGAGAAAAT
16035652 AAACCTAAATGTATG
1 AAACCTAAATGTATG
16035667 AAACCTAAATGTATG
1 AAACCTAAATGTATG
16035682 AAAC
1 AAAC
16035686 GTACAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (15 bp):
AAACCTAAATGTATG
Found at i:16037231 original size:12 final size:12
Alignment explanation
Indices: 16037209--16037238 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
16037199 ATCAAATATT
16037209 AGAACAATAAAGA
1 AGAA-AATAAAGA
16037222 AGAAAATAAAGA
1 AGAAAATAAAGA
16037234 AGAAA
1 AGAAA
16037239 GATGGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (12 bp):
AGAAAATAAAGA
Found at i:16038397 original size:21 final size:22
Alignment explanation
Indices: 16038373--16038421 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
16038363 CACAATGACC
16038373 ACATGCCAAAGT-CACATTCAA
1 ACATGCCAAAGTGCACATTCAA
* * **
16038394 ACATACCAAATTGGTCATTCAA
1 ACATGCCAAAGTGCACATTCAA
16038416 ACATGC
1 ACATGC
16038422 ATTAACCCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (22 bp):
ACATGCCAAAGTGCACATTCAA
Found at i:16039602 original size:20 final size:20
Alignment explanation
Indices: 16039579--16039625 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16039569 ATAGAGACAT
* * *
16039579 CGAAGTGTATACAGGGGCAC
1 CGAAGTGCAAACAAGGGCAC
16039599 CGAAGTGCAAACAAGGGCAC
1 CGAAGTGCAAACAAGGGCAC
16039619 CGAAGTG
1 CGAAGTG
16039626 AAAATCCCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.34, T:0.11
Consensus pattern (20 bp):
CGAAGTGCAAACAAGGGCAC
Found at i:16049201 original size:23 final size:23
Alignment explanation
Indices: 16049156--16049201 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
16049146 TTATTAATAT
* *
16049156 TGTTTGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
16049179 TGTTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTCGATTAA
16049202 GTTAAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.46
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:16052565 original size:17 final size:17
Alignment explanation
Indices: 16052540--16052573 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16052530 CTCCACTCAA
*
16052540 TTAAGCAAGATCTACTC
1 TTAAACAAGATCTACTC
*
16052557 TTAAACAAGGTCTACTC
1 TTAAACAAGATCTACTC
16052574 AACCACCGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
TTAAACAAGATCTACTC
Found at i:16059602 original size:72 final size:74
Alignment explanation
Indices: 16059466--16059603 Score: 235
Period size: 72 Copynumber: 1.9 Consensus size: 74
16059456 GGCATCCATG
16059466 TGTATGCCAAGTTAGCAATTAATTAATTTTTTTAAAAATTAAAAAATATATTTTTATAAACTTTA
1 TGTATGCCAAGTTAGCAATTAATTAATTTTTTTAAAAATTAAAAAATATATTTTTATAAACTTTA
16059531 TTATTAAAA
66 TTATTAAAA
* * *
16059540 TGTATGCCACGTTAGCAATTAATTAA-TTTTTT-AAAATTACAAATTATATTTTTATAAACTTTA
1 TGTATGCCAAGTTAGCAATTAATTAATTTTTTTAAAAATTAAAAAATATATTTTTATAAACTTTA
16059603 T
66 T
16059604 ACTTTTTAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 30 0.49
73 6 0.10
74 25 0.41
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (74 bp):
TGTATGCCAAGTTAGCAATTAATTAATTTTTTTAAAAATTAAAAAATATATTTTTATAAACTTTA
TTATTAAAA
Found at i:16061413 original size:114 final size:114
Alignment explanation
Indices: 16061254--16061461 Score: 271
Period size: 114 Copynumber: 1.8 Consensus size: 114
16061244 ATTAGCAGCT
* * **
16061254 CTTTATCATAAGCACCGCAAAACTATTAAGAAAACGTAGCTGTTTTTCA-TTTATTTTTTCTAGA
1 CTTTATCAGAAGCACCGCAAAACTATTAAGAAAACGTAGCTGTTTTT-AGTTTAGTTTTTAGAGA
* *
16061318 CGTTAGTGGCGATTTTC-AGAAAACGCCGCAGTAGCGAAGCTTTAGTGGCG
65 CGTTAATGGCGATTGTCTA-AAAACGCCGCAGTAGCGAAGCTTTAGTGGCG
* *
16061368 CTTTATCAGAAGCGCCGCAAAACTGTTAAGAAAACG-A-CGTCGTTTTTAGTTTAGTTTTTAGAG
1 CTTTATCAGAAGCACCGCAAAACTATTAAGAAAACGTAGC-T-GTTTTTAGTTTAGTTTTTAGAG
*
16061431 ACGTTAATGGCGCTTGTCTAAAAACGCCGCA
64 ACGTTAATGGCGATTGTCTAAAAACGCCGCA
16061462 AAATATAGGA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
112 1 0.01
113 3 0.04
114 76 0.94
115 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (114 bp):
CTTTATCAGAAGCACCGCAAAACTATTAAGAAAACGTAGCTGTTTTTAGTTTAGTTTTTAGAGAC
GTTAATGGCGATTGTCTAAAAACGCCGCAGTAGCGAAGCTTTAGTGGCG
Found at i:16062105 original size:21 final size:21
Alignment explanation
Indices: 16062079--16062124 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
16062069 TGTTCTTTAA
16062079 TTTA-GGGTTTAAGGGATATGG
1 TTTAGGGGTTT-AGGGATATGG
*
16062100 TTTAGGGGTTTATGGATATGG
1 TTTAGGGGTTTAGGGATATGG
16062121 TTTA
1 TTTA
16062125 AGGATTGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (21 bp):
TTTAGGGGTTTAGGGATATGG
Found at i:16062144 original size:7 final size:7
Alignment explanation
Indices: 16062132--16062183 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
16062122 TTAAGGATTG
16062132 GGGTTAA
1 GGGTTAA
16062139 GGGTTAA
1 GGGTTAA
*
16062146 GGGTTTAG
1 GGG-TTAA
16062154 GGGTTAA
1 GGGTTAA
* *
16062161 GTGCT-A
1 GGGTTAA
16062167 GGGTTAA
1 GGGTTAA
*
16062174 GGGTTTA
1 GGGTTAA
16062181 GGG
1 GGG
16062184 GTTTATAGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
6 4 0.11
7 26 0.72
8 6 0.17
ACGTcount: A:0.21, C:0.02, G:0.46, T:0.31
Consensus pattern (7 bp):
GGGTTAA
Found at i:16062377 original size:21 final size:22
Alignment explanation
Indices: 16062351--16062397 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
16062341 TATGGATTAT
*
16062351 GGTTTAAGGGTT-GGGGTTAAG
1 GGTTTAAGGGTTAAGGGTTAAG
* *
16062372 GGTTTATGGGTTAAGGGTTATG
1 GGTTTAAGGGTTAAGGGTTAAG
16062394 GGTT
1 GGTT
16062398 AGGGGTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (22 bp):
GGTTTAAGGGTTAAGGGTTAAG
Found at i:16062379 original size:28 final size:29
Alignment explanation
Indices: 16062347--16062412 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
16062337 GGCTTATGGA
*
16062347 TTATGGTTTAAGGGTT-GGGGTTAAGGGT
1 TTATGGGTTAAGGGTTAGGGGTTAAGGGT
* *
16062375 TTATGGGTTAAGGGTTATGGGTTAGGGGT
1 TTATGGGTTAAGGGTTAGGGGTTAAGGGT
*
16062404 TTAGGGGTT
1 TTATGGGTT
16062413 TATAGTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (29 bp):
TTATGGGTTAAGGGTTAGGGGTTAAGGGT
Found at i:16062394 original size:14 final size:14
Alignment explanation
Indices: 16062347--16062404 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
16062337 GGCTTATGGA
*
16062347 TTATGGTTTAAGGG
1 TTATGGGTTAAGGG
*
16062361 TT-GGGGTTAAGGG
1 TTATGGGTTAAGGG
16062374 TTTATGGGTTAAGGG
1 -TTATGGGTTAAGGG
*
16062389 TTATGGGTTAGGGG
1 TTATGGGTTAAGGG
16062403 TT
1 TT
16062405 TAGGGGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 9 0.24
14 19 0.50
15 10 0.26
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (14 bp):
TTATGGGTTAAGGG
Found at i:16062414 original size:8 final size:7
Alignment explanation
Indices: 16062313--16062409 Score: 52
Period size: 7 Copynumber: 13.7 Consensus size: 7
16062303 TCTACGATTC
*
16062313 AAGGTTT
1 AAGGGTT
*
16062320 AAGGGAT
1 AAGGGTT
*
16062327 ATGGGTT
1 AAGGGTT
*
16062334 AGAGGCTT
1 A-AGGGTT
* *
16062342 ATGGATT
1 AAGGGTT
* *
16062349 ATGGTTT
1 AAGGGTT
16062356 AAGGGTT
1 AAGGGTT
*
16062363 -GGGGTT
1 AAGGGTT
16062369 AAGGGTTT
1 AAGGG-TT
*
16062377 ATGGGTT
1 AAGGGTT
16062384 AAGGGTT
1 AAGGGTT
*
16062391 ATGGGTT
1 AAGGGTT
*
16062398 AGGGGTT
1 AAGGGTT
*
16062405 TAGGG
1 AAGGG
16062410 GTTTATAGTT
Statistics
Matches: 68, Mismatches: 19, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
6 5 0.07
7 52 0.76
8 11 0.16
ACGTcount: A:0.22, C:0.01, G:0.42, T:0.35
Consensus pattern (7 bp):
AAGGGTT
Found at i:16064276 original size:27 final size:29
Alignment explanation
Indices: 16064222--16064277 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
16064212 ATTTAATTTA
* *
16064222 TATTAAGTTGATTGTTACTTTATCAATTAT
1 TATTAAGTTGATTGTTA-GTGATCAATTAT
16064252 TATTAAGTTGATTGTT-GTGAT-AATTA
1 TATTAAGTTGATTGTTAGTGATCAATTA
16064278 AAATTGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
30 16 0.67
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (29 bp):
TATTAAGTTGATTGTTAGTGATCAATTAT
Found at i:16067573 original size:41 final size:40
Alignment explanation
Indices: 16067517--16067806 Score: 307
Period size: 41 Copynumber: 7.0 Consensus size: 40
16067507 TTGAGATAAA
*
16067517 AAGCACCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTT
* * **
16067558 AAGCGCCGTTAAAGAACATTA-CTTTTCA-CGGCGTTTGTGATAA
1 AAGCGCCGCTAAAGAACATGATC-TTT-AGCGGCGTTT-T--TTT
*
16067601 AAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTTTCGTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT--TT
*
16067643 AAGCGCCGCTAAAGAACATGATCTTTAGCTGCGTCTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTT
* * * *
16067684 AGGCGCCGCTAAAGAACATTA-CTTTTAGCGGCGTTTGTGATA
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT-T-TTT
*
16067726 ATAGCGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTCT
1 A-AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-T
* *
16067768 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
16067807 CTGTAAACGC
Statistics
Matches: 208, Mismatches: 25, Indels: 32
0.78 0.09 0.12
Matches are distributed among these distances:
40 7 0.03
41 96 0.46
42 39 0.19
43 65 0.31
44 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (40 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
Found at i:16067697 original size:126 final size:125
Alignment explanation
Indices: 16067517--16067799 Score: 453
Period size: 126 Copynumber: 2.3 Consensus size: 125
16067507 TTGAGATAAA
* *
16067517 AAGCACCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTAAGCGCCGTTAAAGAACATTACTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTAAGCGCCGCTAAAGAACATTACTT
*
16067582 TTCA-CGGCGTTTGTGATAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCG-TTTTTCGTT
66 TT-AGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC--T
* *
16067643 AAGCGCCGCTAAAGAACATGATCTTTAGCTGCGTCTTTTTTAGGCGCCGCTAAAGAACATTACTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTAAGCGCCGCTAAAGAACATTACTT
* *
16067708 TTAGCGGCGTTTGTGATAATAGCGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTCT
66 TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT
*
16067768 AAGCGCCGCTAAAGAACATGACCTTTAGCGGC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGC
16067800 ATTTTTTCTG
Statistics
Matches: 146, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
125 32 0.22
126 108 0.74
127 6 0.04
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (125 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTAAGCGCCGCTAAAGAACATTACTT
TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT
Found at i:16067754 original size:84 final size:83
Alignment explanation
Indices: 16067517--16067799 Score: 276
Period size: 84 Copynumber: 3.4 Consensus size: 83
16067507 TTGAGATAAA
* * * * *
16067517 AAGCACCGCTAAAGAACATGA-TCTTTAGCGGCGTCTT-T-TTTAAGCGCCGTTAAAGAACATTA
1 AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGT-TTGTCGTAAAGCGCCGCTAAAGAACATGA
* **
16067579 -CTTTTCA-CGGCGTTTGTGATAA
64 TC-TTT-AGCGGCGTTT-T-TTCT
* * *
16067601 AAGCGCCGCTAAAGGACATGA-TCTTTAGCGGCGTTTTTCGTTAAGCGCCGCTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTGTCGTAAAGCGCCGCTAAAGAACATGAT
*
16067665 CTTTAGCTGCGTCTTTTT-T
65 CTTTAGCGGCGT-TTTTTCT
* *
16067684 AGGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTGT-GATAATAGCGCCGCTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTGTCG-TAA-AGCGCCGCTAAAGAACATGA
*
16067748 TTTTTAGCGGCGTTTTTTCT
64 TCTTTAGCGGCGTTTTTTCT
*
16067768 AAGCGCCGCTAAAGAACATGACCTTTAGCGGC
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGC
16067800 ATTTTTTCTG
Statistics
Matches: 172, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
82 1 0.01
83 41 0.24
84 97 0.56
85 30 0.17
86 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (83 bp):
AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTGTCGTAAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTCT
Found at i:16069483 original size:31 final size:31
Alignment explanation
Indices: 16069445--16069510 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
16069435 AACAATCTAA
*
16069445 TGACTTAAATAAAAACTTAT-GAATAGTTAAG
1 TGACTTAAATAAAAACTT-TCAAATAGTTAAG
* *
16069476 TGACTTAAATGAAAACTTTCAAATAGTTTAG
1 TGACTTAAATAAAAACTTTCAAATAGTTAAG
16069507 TGAC
1 TGAC
16069511 CTAATTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTAAG
Found at i:16071519 original size:3 final size:3
Alignment explanation
Indices: 16071499--16071564 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
16071489 GGGTTCCTTG
** *
16071499 TTA TTAA TTA TT- TTA TTA TTA AAA TTAA TTA TTT TTA TTA -TA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
16071544 TTTA TTA TTA TTAA TTA TTA T
1 -TTA TTA TTA TT-A TTA TTA T
16071565 CATATTTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 4 0.08
3 35 0.69
4 12 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:16071548 original size:18 final size:17
Alignment explanation
Indices: 16071499--16071562 Score: 76
Period size: 18 Copynumber: 3.7 Consensus size: 17
16071489 GGGTTCCTTG
16071499 TTATTAATTATTTTATTA
1 TTATTAATTA-TTTATTA
* * *
16071517 TTA-AAATTAATTATTT
1 TTATTAATTATTTATTA
16071533 TTATTATATTATTTATTA
1 TTATTA-ATTATTTATTA
16071551 TTATTAATTATT
1 TTATTAATTATT
16071563 ATCATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 8 0.21
17 12 0.32
18 18 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAATTATTTATTA
Found at i:16071550 original size:21 final size:21
Alignment explanation
Indices: 16071499--16071561 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
16071489 GGGTTCCTTG
16071499 TTATTAATTA-TTTTATTATTA
1 TTATTAATTATTTTTATTA-TA
**
16071520 AAATTAATTATTTTTATTATA
1 TTATTAATTATTTTTATTATA
* *
16071541 TTATTTATTATTATTAATTAT
1 TTATTAATTATT-TTTATTAT
16071562 TATCATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTAATTATTTTTATTATA
Found at i:16071557 original size:31 final size:32
Alignment explanation
Indices: 16071499--16071562 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
16071489 GGGTTCCTTG
16071499 TTATTAATTATTTTATTATTAAAATTAATTATTT
1 TTATTAATTATTTTATTATT--AATTAATTATTT
16071533 TTATTATATTA-TTTATTATT-ATTAATTATT
1 TTATTA-ATTATTTTATTATTAATTAATTATT
16071563 ATCATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 10 0.34
34 15 0.52
35 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTATTAATTATTTTATTATTAATTAATTATTT
Found at i:16071720 original size:13 final size:15
Alignment explanation
Indices: 16071695--16071726 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16071685 TATACGTATG
16071695 TTTTGTTTTTTTA-T
1 TTTTGTTTTTTTACT
16071709 TTTTG-TTTTTTACT
1 TTTTGTTTTTTTACT
16071723 TTTT
1 TTTT
16071727 TATATATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (15 bp):
TTTTGTTTTTTTACT
Found at i:16071747 original size:18 final size:17
Alignment explanation
Indices: 16071723--16071762 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
16071713 GTTTTTTACT
16071723 TTTTTATATATACTTTA
1 TTTTTATATATACTTTA
16071740 TATTTTATATATACTTTA
1 T-TTTTATATATACTTTA
16071758 TTTTT
1 TTTTT
16071763 GTAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTATATATACTTTA
Found at i:16075176 original size:37 final size:38
Alignment explanation
Indices: 16075102--16075177 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
16075092 AACAAGAGTC
16075102 ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
1 ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
*
16075140 ATTATTCTCCTTGGTTAAATGGGAAAAAAA-TCCTTTT
1 ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
16075177 A
1 A
16075178 GCCCTCCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 8 0.22
38 29 0.78
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (38 bp):
ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
Found at i:16082149 original size:26 final size:26
Alignment explanation
Indices: 16082119--16082179 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
16082109 GAAATTTCCA
*
16082119 TTATTTTTCCCCTTCCATTTCTTTCT
1 TTATTTTACCCCTTCCATTTCTTTCT
16082145 TTATTTTACCCCTTCCATTTCTTTCT
1 TTATTTTACCCCTTCCATTTCTTTCT
16082171 TTATTTTAC
1 TTATTTTAC
16082180 AATTGATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTACCCCTTCCATTTCTTTCT
Found at i:16082587 original size:22 final size:25
Alignment explanation
Indices: 16082556--16082601 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 25
16082546 TGAAATTGCT
16082556 TGATGTCGAAAAA-TA-AGAGAAAA
1 TGATGTCGAAAAATTATAGAGAAAA
16082579 TGAT-TCGAAAAATTATAGAGAAA
1 TGATGTCGAAAAATTATAGAGAAA
16082602 GGAAATAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 7 0.33
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (25 bp):
TGATGTCGAAAAATTATAGAGAAAA
Found at i:16086860 original size:45 final size:45
Alignment explanation
Indices: 16086809--16087145 Score: 494
Period size: 45 Copynumber: 7.5 Consensus size: 45
16086799 GATCAAGACA
* *
16086809 AGTAAGACCATAGCTGAAAGATGCTATGGCATCATTATTCAAATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* * * * *
16086854 AGTAAGACTATAGCTGAAAGACGTTATGACATCATTTTTCAGACG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* *
16086899 AGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTTAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* * * **
16086944 AGTAAGACCATAGCTGAAAGACACTATGGCATTATTATTCAAACA
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* *
16086989 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTCAGATA
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
*
16087034 AGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* *
16087079 AGTAAGACCATAGCTGAAAGACGCTATGGAATCATGATTCAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
*
16087124 AGTAAGACCATAGTTGAAAGAC
1 AGTAAGACCATAGCTGAAAGAC
16087146 ATTATAGCAT
Statistics
Matches: 261, Mismatches: 31, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 261 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
Found at i:16087175 original size:90 final size:89
Alignment explanation
Indices: 16086809--16087203 Score: 461
Period size: 90 Copynumber: 4.4 Consensus size: 89
16086799 GATCAAGACA
* * * *
16086809 AGTAAGACCATAGCTGAAAGATGCTATGGCATCATTATTCAAATGAGTAAGACTATAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTCAGATGAGTAAGACCATAGCTGAAAG
* * * * * *
16086874 ACGTTATGACATCATTTTTCAGACG
66 ACATTATGGCATCA-TATTAAAATG
* * *
16086899 AGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTTAGATGAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTCAGATGAGTAAGACCATAGCTGAAAG
* * * **
16086964 ACACTATGGCATTATTATTCAAACA
66 ACATTATGGCATCA-TATTAAAATG
*
16086989 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTCAGATAAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTCAGATGAGTAAGACCATAGCTGAAAG
* * *
16087054 ACGTTATGGCATCATTATTCAGATG
66 ACATTATGGCATCA-TATTAAAATG
* *
16087079 AGTAAGACCATAGCTGAAAGACGCTATGGAATCATGATTCAGATGAGTAAGACCATAGTTGAAAG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTCAGATGAGTAAGACCATAGCTGAAAG
*
16087144 ACATTATAGCATCCA-ATTGAAAATG
66 ACATTATGGCAT-CATATT-AAAATG
* * * *
16087169 AATAAGACCATAG-TGGAAAGGCACTGTGGCATCAT
1 AGTAAGACCATAGCT-GAAAGACGCTATGGCATCAT
16087204 ATCGGAAAGT
Statistics
Matches: 268, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
89 4 0.01
90 262 0.98
91 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (89 bp):
AGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTCAGATGAGTAAGACCATAGCTGAAAG
ACATTATGGCATCATATTAAAATG
Found at i:16087247 original size:46 final size:44
Alignment explanation
Indices: 16087126--16087328 Score: 201
Period size: 46 Copynumber: 4.5 Consensus size: 44
16087116 TTCAGATGAG
* * * * *
16087126 TAAGACCATAGTTGAAAGACATTATAGCATCCAATTGAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAT-CAATGGAAAGTGAA
* * * *
16087171 TAAGACCATAGTGGAAAGGCACTGTGGCATCATATCGGAAAGTGAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCA-AT-GGAAAGTGAA
* * *
16087217 TAAGACCATGGTTGAAATACACTATTGCATCATATCAGAAAGTGAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCA-AT-GGAAAGTGAA
* * *
16087263 TAAGACCATGGTTGAAAGGCATTATGGCATCAAGTGGAGAA-TAAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCAA-TGGA-AAGTGAA
16087308 TAAGACCATGGTTGAAAGACA
1 TAAGACCATGGTTGAAAGACA
16087329 ACATGACATC
Statistics
Matches: 133, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
44 2 0.02
45 53 0.40
46 78 0.59
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (44 bp):
TAAGACCATGGTTGAAAGACACTATGGCATCAATGGAAAGTGAA
Found at i:16087247 original size:91 final size:91
Alignment explanation
Indices: 16087126--16087328 Score: 243
Period size: 91 Copynumber: 2.2 Consensus size: 91
16087116 TTCAGATGAG
* * *
16087126 TAAGACCATAGTTGAAAGACATTATAGCATCCA-AT-TGAAAATGAATAAGACCATAGTGGAAAG
1 TAAGACCATGGTTGAAAGACACTATAGCAT-CATATCAGAAAATGAATAAGACCATAGTGGAAAG
* *
16087189 GCACTGTGGCATCATA-TCGGA-AAGTGAA
65 GCACTATGGCATCA-AGT-GGAGAA-TAAA
* * * * *
16087217 TAAGACCATGGTTGAAATACACTATTGCATCATATCAGAAAGTGAATAAGACCATGGTTGAAAGG
1 TAAGACCATGGTTGAAAGACACTATAGCATCATATCAGAAAATGAATAAGACCATAGTGGAAAGG
*
16087282 CATTATGGCATCAAGTGGAGAATAAA
66 CACTATGGCATCAAGTGGAGAATAAA
16087308 TAAGACCATGGTTGAAAGACA
1 TAAGACCATGGTTGAAAGACA
16087329 ACATGACATC
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
90 2 0.02
91 55 0.57
92 39 0.41
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (91 bp):
TAAGACCATGGTTGAAAGACACTATAGCATCATATCAGAAAATGAATAAGACCATAGTGGAAAGG
CACTATGGCATCAAGTGGAGAATAAA
Found at i:16088781 original size:7 final size:8
Alignment explanation
Indices: 16088753--16088782 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
16088743 TTTCCCAAGT
16088753 TTTTTCGAA
1 TTTTT-GAA
16088762 TTTTTGAA
1 TTTTTGAA
16088770 TTTTTGAA
1 TTTTTGAA
16088778 TTTTT
1 TTTTT
16088783 TCCTTGGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.67
Consensus pattern (8 bp):
TTTTTGAA
Found at i:16092057 original size:20 final size:20
Alignment explanation
Indices: 16092032--16092099 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
16092022 GTGCATATTC
16092032 GTGCTCTTATTAGCACTACG
1 GTGCTCTTATTAGCACTACG
* *
16092052 GTGCTCTTAATAGCACATTC-
1 GTGCTCTTATTAGCAC-TACG
* *
16092072 GTGCTCATGTTAGCACTACG
1 GTGCTCTTATTAGCACTACG
*
16092092 ATGCTCTT
1 GTGCTCTT
16092100 GAAAGCACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.05
20 34 0.89
21 2 0.05
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (20 bp):
GTGCTCTTATTAGCACTACG
Found at i:16092085 original size:40 final size:40
Alignment explanation
Indices: 16092028--16092126 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
16092018 CTGAGTGCAT
* * *
16092028 ATTCGTGCTCTTATTAGCACTACGGTGCTCTT-AATAGCAC
1 ATTCGTGCTCATGTTAGCACTACGATGCTCTTGAA-AGCAC
16092068 ATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAAGCAC
1 ATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAAGCAC
* * *
16092108 ATTCATGCTCCTGATAGCA
1 ATTCGTGCTCATGTTAGCA
16092127 TATTTATGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 50 0.96
41 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (40 bp):
ATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAAGCAC
Found at i:16092106 original size:20 final size:19
Alignment explanation
Indices: 16092043--16092107 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
16092033 TGCTCTTATT
16092043 AGCACTACGGTGCTCTT-AA
1 AGCACTAC-GTGCTCTTGAA
* * **
16092062 TAGCACATTCGTGCTCATGTT
1 -AGCAC-TACGTGCTCTTGAA
16092083 AGCACTACGATGCTCTTGAA
1 AGCACTACG-TGCTCTTGAA
16092103 AGCAC
1 AGCAC
16092108 ATTCATGCTC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 3 0.09
20 29 0.85
21 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (19 bp):
AGCACTACGTGCTCTTGAA
Found at i:16092115 original size:20 final size:20
Alignment explanation
Indices: 16092053--16092140 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 20
16092043 AGCACTACGG
*
16092053 TGCTCTT-AATAGCACATTCG
1 TGCTCTTGAA-AGCACATTCA
* ** *
16092073 TGCTCATGTTAGCAC-TACGA
1 TGCTCTTGAAAGCACATTC-A
16092093 TGCTCTTGAAAGCACATTCA
1 TGCTCTTGAAAGCACATTCA
* * * *
16092113 TGCTCCTGATAGCATATTTA
1 TGCTCTTGAAAGCACATTCA
16092133 TGCTCTTG
1 TGCTCTTG
16092141 TTTGTTTTAC
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.04
20 47 0.92
21 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (20 bp):
TGCTCTTGAAAGCACATTCA
Found at i:16093261 original size:4 final size:4
Alignment explanation
Indices: 16093252--16093285 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
16093242 AACATATTTC
16093252 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
16093286 TCATATCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:16094218 original size:25 final size:25
Alignment explanation
Indices: 16094190--16094320 Score: 102
Period size: 25 Copynumber: 5.2 Consensus size: 25
16094180 TTGGCCACTA
**
16094190 AGGCTTCCCAAATAATAAGTTACAT
1 AGGCTTCCCAAATAATAAGCCACAT
*** * * *
16094215 AGGCTTTTTAAATAACAAGGCACAA
1 AGGCTTCCCAAATAATAAGCCACAT
*
16094240 AGGCTTCCCAAATAATACGCCACAT
1 AGGCTTCCCAAATAATAAGCCACAT
** * *
16094265 AGGCTTTTCAAACAACT-AGCCACAA
1 AGGCTTCCCAAATAA-TAAGCCACAT
* *
16094290 AGGCTTTCCAAATAATATGCCACAT
1 AGGCTTCCCAAATAATAAGCCACAT
*
16094315 AAGCTT
1 AGGCTT
16094321 TCTAGATAGC
Statistics
Matches: 80, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
24 1 0.01
25 78 0.98
26 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (25 bp):
AGGCTTCCCAAATAATAAGCCACAT
Found at i:16094251 original size:50 final size:50
Alignment explanation
Indices: 16094183--16094321 Score: 179
Period size: 50 Copynumber: 2.8 Consensus size: 50
16094173 AGATAACTTG
* ** * *
16094183 GCCACTAAGGCTTCCCAAATAATAAGTTACATAGGCTTTTTAAATAACAA
1 GCCACAAAGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAACAACAA
* * *
16094233 GGCACAAAGGCTTCCCAAATAATACGCCACATAGGCTTTTCAAACAACTA
1 GCCACAAAGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAACAACAA
* * *
16094283 GCCACAAAGGCTTTCCAAATAATATGCCACATAAGCTTT
1 GCCACAAAGGCTTCCCAAATAATAAGCCACATAGGCTTT
16094322 CTAGATAGCC
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (50 bp):
GCCACAAAGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAACAACAA
Found at i:16094341 original size:21 final size:22
Alignment explanation
Indices: 16094235--16094341 Score: 58
Period size: 25 Copynumber: 4.5 Consensus size: 22
16094225 AATAACAAGG
*
16094235 CACAAAGGCTTCCCAAATAATACGC
1 CACAAAGGCTTTCC--ATAATA-GC
* * *
16094260 CACATAGGCTTTTCAAACAACTAGC
1 CACAAAGGC-TTTC-CATAA-TAGC
16094285 CACAAAGGCTTTCCAAATAATATGC
1 CACAAAGGCTTTCC--ATAATA-GC
16094310 CACATAA-GCTTT-C-TAGATAGC
1 CACA-AAGGCTTTCCATA-ATAGC
16094331 CACAAAGGCTT
1 CACAAAGGCTT
16094342 ATTTGGTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
20 2 0.03
21 12 0.18
22 3 0.05
24 7 0.11
25 35 0.53
26 7 0.11
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.22
Consensus pattern (22 bp):
CACAAAGGCTTTCCATAATAGC
Found at i:16099352 original size:26 final size:27
Alignment explanation
Indices: 16099300--16099356 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
16099290 AAAGGTTGCT
*
16099300 AAATGACCAAAATACCCTCGGAGGGTA
1 AAATGACCAAAATACCCTCAGAGGGTA
*
16099327 AAATGACCAAAATACCCTTAGA-GGTA
1 AAATGACCAAAATACCCTCAGAGGGTA
16099353 AAAT
1 AAAT
16099357 TATCGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCTCAGAGGGTA
Found at i:16103691 original size:20 final size:20
Alignment explanation
Indices: 16103666--16103704 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
16103656 TGGAAAAACC
16103666 ACTCTTCCGTTAACCACTCA
1 ACTCTTCCGTTAACCACTCA
16103686 ACTCTTCCGTTAACCACTC
1 ACTCTTCCGTTAACCACTC
16103705 TCACATCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.41, G:0.05, T:0.31
Consensus pattern (20 bp):
ACTCTTCCGTTAACCACTCA
Found at i:16119217 original size:42 final size:41
Alignment explanation
Indices: 16119087--16119310 Score: 168
Period size: 42 Copynumber: 5.3 Consensus size: 41
16119077 ATTCAACACT
* *
16119087 TAGCAACCACC-TTAAATTCAGTGATACG-GAGAATCAGCACA
1 TAGCAACC-CCTTTATATTCAGTTATACGAG-GAATCAGCACA
* * * *** *
16119128 TAGTAACCCCTTTCACAATCAAAGATACG-GTAGAATCAGCACT
1 TAGCAACCCCTTT-ATATTCAGTTATACGAG--GAATCAGCACA
*
16119171 TAGCAGCCACCTTTATATTCAGTTATACGAGGAATCAGCACA
1 TAGCAACC-CCTTTATATTCAGTTATACGAGGAATCAGCACA
* * ** *
16119213 TAGCAACCCCTTTCACAATCAAATATACGATGGAATCAACAC-
1 TAGCAACCCCTTT-ATATTCAGTTATACGA-GGAATCAGCACA
* * *
16119255 TAAGCAACCACCTTTATATTCAGTGATAAGGGGAATCAGCACA
1 T-AGCAACC-CCTTTATATTCAGTTATACGAGGAATCAGCACA
16119298 TAGCAACCCCTTT
1 TAGCAACCCCTTT
16119311 CAAAATCAAA
Statistics
Matches: 145, Mismatches: 28, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
40 2 0.01
41 19 0.13
42 59 0.41
43 54 0.37
44 11 0.08
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (41 bp):
TAGCAACCCCTTTATATTCAGTTATACGAGGAATCAGCACA
Found at i:16119225 original size:85 final size:84
Alignment explanation
Indices: 16119083--16119346 Score: 370
Period size: 85 Copynumber: 3.1 Consensus size: 84
16119073 GTGGATTCAA
* *
16119083 CACTTAGCAACCACC-TTAAATTCAGTGATACGGAGAATCAGCACATAGTAACCCCTTTCACAAT
1 CACTTAGCAACCACCTTTATATTCAGTGATACGG-GAATCAGCACATAGCAACCCCTTTCACAAT
*
16119147 CAAAGATACGGTAGAATCAG
65 CAAATATACGGTAGAATCAG
* *
16119167 CACTTAGCAGCCACCTTTATATTCAGTTATACGAGGAATCAGCACATAGCAACCCCTTTCACAAT
1 CACTTAGCAACCACCTTTATATTCAGTGATACG-GGAATCAGCACATAGCAACCCCTTTCACAAT
* * *
16119232 CAAATATACGATGGAATCAA
65 CAAATATACGGTAGAATCAG
* * *
16119252 CACTAAGCAACCACCTTTATATTCAGTGATAAGGGGAATCAGCACATAGCAACCCCTTTCAAAAT
1 CACTTAGCAACCACCTTTATATTCAGTGAT-ACGGGAATCAGCACATAGCAACCCCTTTCACAAT
*
16119317 CAAATATACAGTCA-AATCAG
65 CAAATATACGGT-AGAATCAG
16119337 CACTTAGCAA
1 CACTTAGCAA
16119347 GCCCTTGGGG
Statistics
Matches: 158, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
84 14 0.09
85 141 0.89
86 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (84 bp):
CACTTAGCAACCACCTTTATATTCAGTGATACGGGAATCAGCACATAGCAACCCCTTTCACAATC
AAATATACGGTAGAATCAG
Found at i:16119345 original size:43 final size:42
Alignment explanation
Indices: 16119117--16119352 Score: 171
Period size: 43 Copynumber: 5.5 Consensus size: 42
16119107 GTGATACGGA
* * *
16119117 GAATCAGCACATAGTAACCCCTTTCACAATCAAAGATACGGT
1 GAATCAGCACATAGCAACCCCTTTCACAATCAAATATACAGT
* * * * **
16119159 AGAATCAGCACTTAGCAGCCACCTTT-ATATTCAGTTATACGAG-
1 -GAATCAGCACATAGCAACC-CCTTTCACAATCAAATATAC-AGT
16119202 GAATCAGCACATAGCAACCCCTTTCACAATCAAATATAC-GAT
1 GAATCAGCACATAGCAACCCCTTTCACAATCAAATATACAG-T
* * * * *
16119244 GGAATCAACAC-TAAGCAACCACCTTT-ATATTC-AGTGATA-AGGG
1 -GAATCAGCACAT-AGCAACC-CCTTTCACAATCAAAT-ATACA-GT
*
16119287 GAATCAGCACATAGCAACCCCTTTCAAAATCAAATATACAGT
1 GAATCAGCACATAGCAACCCCTTTCACAATCAAATATACAGT
* * *
16119329 CAAATCAGCACTTAGCAAGCCCTT
1 -GAATCAGCACATAGCAACCCCTT
16119353 GGGGAATCTG
Statistics
Matches: 149, Mismatches: 28, Indels: 32
0.71 0.13 0.15
Matches are distributed among these distances:
40 1 0.01
41 10 0.07
42 54 0.36
43 72 0.48
44 12 0.08
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.23
Consensus pattern (42 bp):
GAATCAGCACATAGCAACCCCTTTCACAATCAAATATACAGT
Found at i:16122699 original size:42 final size:42
Alignment explanation
Indices: 16122619--16122700 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
16122609 CGTTTTCTCT
* **
16122619 ATGCCATAGTCCAACTATGGTCTTACACATGTTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATGTGCACATATTG
*
16122661 ATGCCATAGCCCAGCTATGGTCTTACACA-GTAGCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACATGT-GCACATAT
16122701 CACACCAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATGTGCACATATTG
Found at i:16125332 original size:43 final size:43
Alignment explanation
Indices: 16125205--16125345 Score: 137
Period size: 43 Copynumber: 3.3 Consensus size: 43
16125195 ATCCGTTACT
* *
16125205 CGGTGGATTCAGCACTTAGCAACCA-CATTAAATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATA
** * * **
16125247 CGG-GGAATCAGCACACAGCAACC-CCTTTCACAGTCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-AAATTCAGTGATA
* * *
16125289 CGGTGGAATCAACAGTTATCAACCACCTTTAAATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATA
*
16125332 CGG-AGAATCAGCAC
1 CGGTGGAATCAGCAC
16125346 ACCTTTAGTA
Statistics
Matches: 75, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
41 20 0.27
42 23 0.31
43 27 0.36
44 5 0.07
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATA
Found at i:16125775 original size:30 final size:30
Alignment explanation
Indices: 16125727--16125785 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
16125717 TCCTTAACTC
*
16125727 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTACCCCT
* * * *
16125757 AAACTTTTGCATATTTACACTTTTACCCC
1 AAACTTTTGAAAAATTACAATTTTACCCC
16125786 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTACCCCT
Found at i:16132830 original size:13 final size:13
Alignment explanation
Indices: 16132812--16132838 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16132802 ATATGGGTAC
16132812 CCCTGTGTTGTGA
1 CCCTGTGTTGTGA
16132825 CCCTGTGTTGTGA
1 CCCTGTGTTGTGA
16132838 C
1 C
16132839 ACACAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.26, G:0.30, T:0.37
Consensus pattern (13 bp):
CCCTGTGTTGTGA
Found at i:16133930 original size:12 final size:12
Alignment explanation
Indices: 16133913--16133939 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16133903 CACACGCCCG
16133913 TGTGCTAGGCCA
1 TGTGCTAGGCCA
16133925 TGTGCTAGGCCA
1 TGTGCTAGGCCA
16133937 TGT
1 TGT
16133940 AACTCACTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (12 bp):
TGTGCTAGGCCA
Found at i:16134831 original size:20 final size:21
Alignment explanation
Indices: 16134792--16134831 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16134782 TACATCAATT
*
16134792 AGATCATGCATTCTTTCCATA
1 AGATCATGCATTCATTCCATA
*
16134813 AGATCATGC-TTGATTCCAT
1 AGATCATGCATTCATTCCAT
16134832 TTGAATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (21 bp):
AGATCATGCATTCATTCCATA
Found at i:16138039 original size:14 final size:14
Alignment explanation
Indices: 16138020--16138046 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16138010 TCAAATGACA
16138020 TAGGTATTTATGAG
1 TAGGTATTTATGAG
16138034 TAGGTATTTATGA
1 TAGGTATTTATGA
16138047 TTGATGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
TAGGTATTTATGAG
Found at i:16148424 original size:103 final size:103
Alignment explanation
Indices: 16148246--16148614 Score: 488
Period size: 103 Copynumber: 3.6 Consensus size: 103
16148236 TAACCGTTAT
* * ** * ** *
16148246 CGGTGGATTCTGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
* * * *
16148311 GAATCAGCACTTAGCAACCCCC-TTCACAATTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * * *
16148348 CGGTGGAACCATCACTTAGCAACCACCAAATGGGTTGGGGAGTCAGCACTTAGCAACCCCTCGGG
1 CGGTGGAATCAGCACTTAGCAACCACC-AATGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGG
16148413 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
65 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* *
16148452 CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
16148517 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * ** * * **
16148555 TGGTGGGATCAGCACTTAGCAACCACCAATGAATAGGGAAATTAGCACACAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGGGTAGGGGAATCAGCACTTAGCAACCCCT
16148615 TTATATGCAA
Statistics
Matches: 235, Mismatches: 30, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
102 23 0.10
103 176 0.75
104 36 0.15
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:16150465 original size:138 final size:138
Alignment explanation
Indices: 16150170--16150748 Score: 788
Period size: 138 Copynumber: 4.2 Consensus size: 138
16150160 ACATAGATAA
* *
16150170 AATTAATATGTAAATTTGATTCATACAAAAATATTAATTATATATATTTTACCGAATTTATTAAT
1 AATTAATATATGAATTTGATTCATAC-AAAATATTAATTATATATATTTTACCGAATTTATTAAT
* * * ** *
16150235 ATAGACAGTTATATTAATTTAATTTAAAATCAAAATATAAAAGATGT-GAAAATTAATGTTCTTT
65 ATAAACAATTATATTAA-TTAATTT-CAATCAAAATATAAAAGACATAG-AAATTAATATTCTTT
*
16150299 TGAAAAGAATAT
127 TGGAAAGAATAT
* *
16150311 AATTAATATATGAATTTGGTTCATACAAAATATTAATTATATATATTTGACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
* * * *
16150376 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAATACATAGAAGTTAATATTCATTTGGA
66 TAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATAGAAATTAATATTCTTTTGGA
16150441 AAGAATAT
131 AAGAATAT
* * * *
16150449 AATTAATATATGAATTTAATTCATACAAAATATTAATTTTATATATTTTATCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
* * * * ** * *
16150514 TGAATAGTTAGATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTTTTTTGGA
66 TAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATAGAAATTAATATTCTTTTGGA
16150579 AAGAATAT
131 AAGAATAT
* * * *
16150587 AATTAATATTTAAATTTGATTCATACAAAATATTAATTTTATATATTTTACTGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
*
16150652 T-AA-AATTATATT-ATTGAATTTCAATCAAAATATAAAAGACATATAAATTAATATTCTTTTGG
66 TAAACAATTATATTAATT-AATTTCAATCAAAATATAAAAGACATAGAAATTAATATTCTTTTGG
16150714 AAAGAATAT
130 AAAGAATAT
*
16150723 AATTAATATAAGAATTTGATTCATAC
1 AATTAATATATGAATTTGATTCATAC
16150749 TGTAAAAGCT
Statistics
Matches: 387, Mismatches: 49, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
135 3 0.01
136 80 0.21
137 2 0.01
138 219 0.57
139 8 0.02
140 52 0.13
141 23 0.06
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
TAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATAGAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:16156864 original size:50 final size:51
Alignment explanation
Indices: 16156804--16156922 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 51
16156794 GGACACACCA
* * * * * *
16156804 CAGCTTGTATGAGATTACCGATTTGCAACTCTTGAGAGCTTACCAATTC-T
1 CAGCTCGTATGACATTACAGATTTACAACTCGTGAGAGCATACCAATTCAT
* * * *
16156854 CAGCTCGTATGACCTTACAGATTTACAGCTCGTGAGAGCATATCGATTCAT
1 CAGCTCGTATGACATTACAGATTTACAACTCGTGAGAGCATACCAATTCAT
*
16156905 -AGCTCGTATGACCTTACA
1 CAGCTCGTATGACATTACA
16156923 TGTACAGGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 57 0.98
51 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (51 bp):
CAGCTCGTATGACATTACAGATTTACAACTCGTGAGAGCATACCAATTCAT
Found at i:16156870 original size:25 final size:25
Alignment explanation
Indices: 16156842--16156921 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
16156832 CTCTTGAGAG
16156842 CTTACCAATTCTCAGCTCGTATGAC
1 CTTACCAATTCTCAGCTCGTATGAC
*
16156867 CTTA-CAGATT-TACAGCTCGTGA-GAG
1 CTTACCA-ATTCT-CAGCTCGT-ATGAC
* * *
16156892 CATATCGATTCAT-AGCTCGTATGAC
1 CTTACCAATTC-TCAGCTCGTATGAC
16156917 CTTAC
1 CTTAC
16156922 ATGTACAGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 4 0.10
25 35 0.83
26 2 0.05
27 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (25 bp):
CTTACCAATTCTCAGCTCGTATGAC
Done.